Tools and Services
EurOPDX Data Portal provides you with a unique environment for data browsing and analysis of PDX mice models across the EurOPDX consortium.
Watch the recording of our webinar on 23rd October 2019 for an introduction to the EurOPDX Data Portal or read the instructions below.
We are at the beginning of a long journey to a robust research infrastructure that will provide the researchers with on-demand tools chained into appropriate pipelines. We apology in advance for any inconvenience which can be caused by the development and maintenance of the Data Portal.
EurOPDX cBioPortal for Cancer Genomics
EurOPDX consortium is one of the adopters of cBioPortal for Cancer Genomics from Memorial Sloan Kettering Cancer Center (MSK).
cBioPortal is a web-based platform enabling researchers to browse, explore, visualize and analyze large-scale cancer genomics datasets.
As the PDX researchers within the EurOPDX consortium produce molecular profiling data from human and mouse tumor and cancer tissue, cBioPortal converts these data into a better understandable and accessible genetic, epigenetic, gene expression and proteomic events. Every step of the analysis is interactive and enables users - for example - to compare their data with different collections (studies) from their colleagues across the consortium.
People working with PDX mice models have a possibility to specify a wide range of properties of a model tumor or tissue and differentiate it from the human samples.
We are now focused on the collection of the molecular profiling data from EurOPDX partners and connecting the EurOPDX cBioPortal instance with the newly released EurOPDX Data Portal as an on-demand tool. The researcher comes to EurOPDX Data Portal, selects mice models of interest and after that can transfer the molecular profiling data of the desired models into a new cBioPortal instance created on his/her demand. For detailed instructions on how to manage this, please, scroll down.
1. Click on Search item in the top menu. Alternativelly you can click on "Explore the EurOPDX data" button on the Data Portal home page.
2. You will be asked to log in to the system. More information about log in and registration process you can find here.
3. In the Search section you can select PDX models according to parameters specified in filter on the left side. To explore the selected models in cBioPortal click on Export to cBioPortal.
4. Then a page with data statistics will be displayed. By clicking on Export data button the export to cBioPoral will be started.
5. The process can take several minutes - a status bar will be displayed to inform you about the progress.
6. Once the data is succesfully exported to cBioPortal, by clicking on cBio Portal button you will start a cBioPortal instance with the selected data.
7. In the cBioPortal you can explore and analyze the selected data. For using cBioPortal platform please read the cBioPortal user's guide.
8. By clicking on your login name on the top right you can see the User Dashboard with list of all your active cBioPortal instances. After clicking on an instance's ID this cBioPortal instance will be relaunched.
9. In your User Dashboard you can extend the instance's lifetime - click on "Settings" button, then specify the time ("minutes" or "hours:minutes") and click on Increase. You can also delete an instance by clicking on Delete button.
Examples of both EurOPDX Data Portal and EurOPDX cBioPortal usage can be found in nascent user documentation here.